Protex-A Python utility for proton exchange in molecular dynamics simulations

Protex is an open-source program that enables proton exchanges of solvent molecules during molecular dynamics simulations. While conventional molecular dynamics simulations do not allow for bond breaking or formation, protex offers an easy-to-use interface to augment these simulations and define multiple proton sites for (de-)protonation using a single topology approach with two different λ-states. Protex was successfully applied to a protic ionic liquid system, where each molecule is prone to (de-)protonation. Transport properties were calculated and compared to experimental values and simulations without proton exchange.

ReaxFF-based nonadiabatic dynamics method for azobenzene derivatives

ReaxFF reactive force fields have been parameterized for the ground and first excited states of azobenzene and its derivatives. In addition, an extended set of ab initio reference data ensures wide applicability, including to azosystems in complex environments. Based on the optimized force fields, nonadiabatic surface hopping simulations produce photoisomerization quantum yields and decay times of azobenzene, both in the gas phase and in n-hexane solution, in reasonable agreement with higher level theory and experiment. The transferability to other azo-compounds is illustrated for different arylazopyrazoles as well as ethylene-bridged azobenzene. Moreover, it has been shown that the model can be easily extended to adsorbates on metal surfaces. The simulation of the ring-opening of cyclobutene triggered by the photoisomerization of azobenzene in a macrocycle highlights the advantages of a reactive force field model.

Polarizable molecular dynamics simulations on the conductivity of pure 1-methylimidazolium acetate systems

The protic ionic liquid 1-methylimidazolium acetate is in equilibrium with its neutral species 1-methylimidazole and acetic acid. Although several experimental data indicate that the equilibrium favors the neutral species, the system exhibits a significant conductivity. We developed a polarizable force field to describe the ionic liquid accurately and applied it to several mixtures of the neutral and charged species. In addition to comparing single values, such as density, diffusion coefficients, and conductivity, with experimental data, the complete frequency-dependent dielectric spectrum ranging from several MHz to THz can be used to determine the equilibrium composition of the reaction mentioned above.